Project Summary The outcome of Herpes Simplex Virus type 1 (HSV-1) disease depends heavily on whether neuronal replication phenotypes trend towards a productive or silent infection. However, the variables which govern these heterologous infection phenotypes are not fully understood. Identification of factors which influence the outcome of neuronal replication is essential to develop new treatments for severe disease and alleviate the global burden of HSV-1. A major limitation to the study of heterologous infection phenotypes is that they are quickly lost in traditional culture models, typically being overwhelmed by secondary viral spread from productively infected cells. Our solution to this problem is to incorporate drop-based microfluidic technology that allows detection of diverse viral replication outcomes with single-cell resolution. We have developed a method to grow and infect primary neurons using a micron-scale, hydrogel bead (microgel), that permits single-cell experimentation within an isolated environment. Our proposal aims to investigate the conditions and factors that give rise to heterologous outcomes of neuronal HSV-1 infection with the ultimate goal of better understanding the determinants of HSV-1 disease. This proposal will combine the development and characterization of in-drop neuronal infection to address critical questions about HSV-1 infection and disease. The first aim will focus on classifying the outcomes of viral replication in different neuron types. The second will use single-cell transcriptional profiling of infected neurons to identify transcripts that promote productive or silent HSV-1 infection. Specific Aim 1 focuses on quantifying heterologous phenotypes of HSV-1 infection in neurons. We will utilize drop-based microfluidic separation and analysis of HSV-1 infected neurons. Outcomes of viral infection will be measured by HSV-1- expressed fluorescent proteins and in-drop PCR detection of viral genomes. We expect that the extent of viral replication reflects the capacity for different cellular environments to support HSV-1 infection. Specific Aim 2 focuses on single cell transcriptional profiling of productive or silent HSV-1 replication in neurons. We will implement in-drop single-cell RNA-sequencing to profile viral and cellular transcripts from infected neurons. Clustering analysis and classification of single cell transcriptomes will be based on the detection of viral RNAs. The presence of individual transcripts will reflect the extent of viral replication occurring in each cell. Following classification, correlation analysis will identify cellular transcripts that are increased or decreased with each infection state. Together, these experiments will identify and quantify the range of outcomes for HSV-1 infection of neurons. Subsequently, we will discover cellular genes that promote or inhibit productive viral replication by identifying determinants of certain heterologous phenotypes. Exploring neuronal in...